Drivers of reef fish carbonate production and composition
Mattia Ghilardi1, Michael A Salter2, Chris T Perry2, Rod W Wilson2, Valeriano Parravicini3, Sebastian CA Ferse1, Tim Rixen4, Christian Wild5, David Mouillot6, Sonia Bejarano1
1) Department of Ecology, Leibniz Centre for Tropical Marine Research (ZMT), Fahrenheitstraße 6, 28359 Bremen, Germany; 2)Geography, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4RJ, UK; 3) PSL Université Paris: EPHE-UPVD-CNRS, USR3278 CRIOBE, University of Perpignan, 66860 Perpignan, France; 4) Department of Biogeochemistry and Geology, Leibniz Centre for Tropical Marine Research (ZMT), Fahrenheitstraße 6, 28359 Bremen, Germany; 5) Department of Marine Ecology, Faculty of Biology and Chemistry, University of Bremen, Leobener Straße UFT, 28359 Bremen, Germany; 6) MARBEC, University of Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France
Marine teleosts produce and excrete carbonate precipitates at high rates (up to 105 g m-2 yr-1 on reefs), thereby substantially contributing to carbonate production in the ocean. Large-scale models are therefore required to understand the role of fish in the marine inorganic carbon cycle. Some global and regional estimates exist, however, they have been produced as a function of fish biomass and water temperature, assuming a close relationship between carbonate excretion and metabolism. The factors influencing interspecific differences in excretion rate and mineralogical composition of fish carbonate have yet to be investigated. Here, we combine published data from The Bahamas and Australia with new data from Palau to create the largest fish carbonate database available to date. Then, we model carbonate excretion rates and mineralogy as a function of biological and environmental variables to: (1) determine the main drivers of production and composition; (2) assess the direction and strength of the relationships; and (3) build predictive models useful for future macroecological studies. We reveal that fish carbonate production is strongly influenced by metabolic rate. Particularly, excretion rates are mainly driven by body size, but also positively related to water temperature and fish activity level. Moreover, fish intestinal length negatively affects carbonate production, suggesting that longer retention times reduce excretion rates. Overall, these patterns are consistent among different carbonate polymorphs produced by fishes and the mineralogical composition is generally strongly conserved within taxonomic families. Ultimately, the high accuracy of our models in predicting both production and composition of fish carbonates paves the way for future macroecological studies.
The estimation of recent demography in a coral reef fish (Hypoplectrus puella) using IBD-Blocks
Nina Tombers1,2, Martin Helmkampf2, Oscar Puebla1,2
1Carl von Ossietzky University of Oldenburg, Ammerländer Heerstraße 114-118, 26129 Oldenburg
2Leibniz Centre for Tropical Marine Research (ZMT), Fahrenheitstraße 6, 28359 Bremen
Dispersal and effective population size are two fundamental parameters for the ecology, management and conservation of coral reef fishes. Nevertheless, these two parameters are notoriously difficult to estimate. With the advent of next-generation DNA sequencing, we can now identify blocks of Identity-By-Descent (IBD) from whole-genome data. IBD blocks are stretches of DNA that are transmitted in one piece from one generation to the next. They are broken down by recombination, becoming shorter every generation. Their number and length provides therefore an opportunity to infer recent demography, including effective populations size and also dispersal when samples are taken continuously across the landscape. Nevertheless, to the best of my knowledge, this approach has only been applied to human populations so far. For my master’s thesis, I want to leverage a dataset of 48 barred hamlet (Hypoplectrus puella) genomes sampled continuously along the Mesoamerican Barrier Reef in Belize to estimate recent effective population size and dispersal from IBD blocks. I genotyped the 48 genomes, explored the different bioinformatic methods available to identify IBD blocks, and applied the most appropriate one to my dataset. I will now use these IBD blocks to estimate dispersal and effective population size. Preliminary analyses suggest that IBD blocks reveal a subtle pattern of genetic isolation by distance that may be used to estimate dispersal.
A Genomic Clock to predict Lifespan in Fish
Finn Opätz1,2, Martin Helmkampf2, Oscar Puebla2,3
1The University of Bremen, Bibliothekstraße 1, 28359 Bremen
2Leibniz Centre for Tropical Marine Research (ZMT), Fahrenheitstraße 6, 28359 Bremen
3Carl von Ossietzky University of Oldenburg, Ammerländer Heerstraße 114-118, 26129 Oldenburg
Maximum lifespan is a fundamental parameter for the dynamics of fish populations. Nevertheless, the maximum lifespan of the vast majority of fishes is unknown. Recently, a genomic clock has been developed to predict maximum lifespan in vertebrates. It is based on the density of cytosine-phosphate-guanine (CpG) motifs in a selected set of human promoters. The maximum lifespans predicted by this approach correlate well with the known maximum lifespans in mammals (R2 between the two = 0.91), but less so in fishes (R2 = 0.56). In the scope of my student research project, I applied the vertebrate clock to the barred hamlet (Hypoplectrus puella) and obtained a lifespan estimate 30 years, which is high but not uncommon for reef fishes. I also applied it to the most closely related species for which both a genome and a maximum lifespan are available and obtained an estimate of 25 years from the molecular clock, which is very close to the known maximum estimate of 26 years. In light if these encouraging results, I decided to develop a new genomic clock with a set of fish promoters for my Master’s thesis, and test whether it provides a better correlation between estimated and known maximum lifespans in fishes. Such a clock would provide the opportunity to generate maximum lifespan estimates for hundreds of fish species for which a genome is available.
MorFishJ: A software package for semi-automatic fish morphometric analysis from side view images
Department of Ecology, Leibniz Centre for Tropical Marine Research (ZMT), Fahrenheitstraße 6, 28359 Bremen, Germany
The last decade has seen a rapid increase in the number of large published phenotypic fish datasets which allowed to address macroecological and macroevolutionary questions previously unattainable. The creation of such databases involved enormous researcher effort, however, the lack of a standardised data acquisition protocol across studies makes it impractical to merge them and limits their extensibility. While advances in modern morphometrics (landmarks configuration and outline analysis) have increasingly facilitated data acquisition and analysis, traditional morphometrics has not kept pace. Yet, it remains central to study fish communities and their responses to natural or anthropogenic changes through trait-based approaches. Here, we present MorFishJ, an open-source software package that allows users to measure a complete suite of morphological traits from side view fish images through a semi-automated procedure. MorFishJ has been developed as a plugin for the open-source software ImageJ to facilitate accessibility to the whole research community and adaptability for specific needs. Three separate analyses (complete morphometric characterisation, measurement of head angles, and analysis of gut morphology) can be performed on single or multiple images and across multiple working sessions without losing progress. Results are saved in a ready-to-use format suitable for statistical analysis with multiple software. The code structure is designed to facilitate software extensibility by adding traits to existing analyses or implementing new analysis targeting specific body parts (e.g. fins) or unusual morphologies (e.g. flatfishes, eels) that could benefit the fish research community. With MorFishJ we aim to accelerate morphometric data acquisition, while increasing reproducibility and data accuracy by reducing user bias. Furthermore, this tool provides standardised data acquisition that makes it extremely easy to combine data from multiple studies and build a global database that can open avenues for future macroecological and macroevolutionary studies.
Figure © Mattia Ghilardi